Bug fix in VCF to table protocol
Added paramter for the latest dbSNP version.
Merge pull request #33 from pneerincx/master

Added parameter for the latest dbSNP version.
Fixed bugs in GAF/Bcl2Fastq workflow: added missing params for CreateFinalReport step and improved handling of tmp dirs to make it compatible with both local execution as well as running on a cluster node.
Merge pull request #34 from pneerincx/master

Fixed bugs in GAF/Bcl2Fastq workflow.
fixed conflict in merge
Improvements to creation of final reports per sample.
Fixed lot's of typos related to different env on new server.
Merge pull request #35 from pneerincx/master

Small fixes for the GAF data archiving workflow.
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Small fixes for the data archiving workflow; Changed temp dir for bcl2fastq conversion to on where we do have write access and added AGI as barcodeType.
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines

Regular pull from blessed master.
Merge pull request #36 from pneerincx/master

Small fixes for the data archiving workflow.
fixing aborted pull
Polished Demultiplex.ftl by moving some repeating code into custom functions/subs.
Merge pull request #37 from pneerincx/master

Improved demultiplex protocol
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Included DataTransfer.sh.ftl in standard NGS_alignment pipeline.
Merge pull request #38 from freerkvandijk/master

Added dataTransfer protocol
Update on MergeIndelCalls protocol. Sorting of VCF file now done in separate perl script.